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Germylenes: structures, electron affinities, and singlet-triplet gaps of the conventional XGeCY(3) (X = H, F, Cl, Br, and I; Y = F and Cl) species and the unexpected cyclic XGeCY(3) (Y = Br and I) systems

Bundhun A, Abdallah HH, Ramasami P, Schaefer HF

J Phys Chem A, 2010 Dec 23;114(50):13198-212.
PMID: 21090692 DOI: 10.1021/jp1078955

A systematic investigation of the X-Ge-CY(3) (X = H, F, Cl, Br, and I; Y = F, Cl, Br, and I) species is carried out using density functional theory. The basis sets used for all atoms (except iodine) in this work are of double-ζ plus polarization quality with additional s- and p-type diffuse functions, and denoted DZP++. Vibrational frequency analyses are performed to evaluate zero-point energy corrections and to determine the nature of the stationary points located. Predicted are four different forms of neutral-anion separations: adiabatic electron affinity (EA(ad)), zero-point vibrational energy corrected EA(ad(ZPVE)), vertical electron affinity (EA(vert)), and vertical detachment energy (VDE). The electronegativity (χ) reactivity descriptor for the halogens (X = F, Cl, Br, and I) is used as a tool to assess the interrelated properties of these germylenes. The topological position of the halogen atom bound to the divalent germanium center is well correlated with the trend in the electron affinities and singlet-triplet gaps. For the expected XGeCY(3) structures (X = H, F, Cl, Br, and I; Y = F and Cl), the predicted trend in the electron affinities is well correlated with simpler germylene derivatives (J. Phys. Chem. A 2009, 113, 8080). The predicted EA(ad(ZPVE)) values with the BHLYP functional range from 1.66 eV (FGeCCl(3)) to 2.20 eV (IGeCF(3)), while the singlet-triplet splittings range from 1.28 eV (HGeCF(3)) to 2.22 eV (FGeCCl(3)). The XGeCY(3) (Y = Br and I) species are most often characterized by three-membered cyclic systems involving the divalent germanium atom, the carbon atom, and a halogen atom.
Fulltext Synthesis, Biological Evaluation and Molecular Docking Studies of 6-Aryl-2-Styrylquinazolin-4(3H)-Ones

Agbo EN, Makhafola TJ, Choong YS, Mphahlele MJ, Ramasami P

Molecules, 2015 Dec 25;21(1):E28.
PMID: 26712730 DOI: 10.3390/molecules21010028

Suzuki-Miyaura cross-coupling of 6-bromo-2-styrylquinazolin-4(3H)-ones with arylboronic acids afforded a series of novel 6-aryl-2-styrylquinazolin-4(3H)-ones. These compounds were evaluated for potential anticancer properties against the human renal (TK-10), melanoma (UACC-62) and breast cancer (MCF-7) cell lines. Their antimicrobial properties were also evaluated against six Gram-positive and four Gram-negative bacteria, as well as two strains of fungi. Molecular docking studies (in silico) were conducted on compounds 5a, b, d and 6a, b, d-f to recognize the hypothetical binding motif of the title compounds within the active site of the dihydrofolate reductase and thymidylate synthase enzymes.
Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R

Choong YS, Lim YY, Soong JX, Savoo N, Guida C, Rhyman L, et al.

Hormones (Athens), 2021 Sep;20(3):557-569.
PMID: 33782920 DOI: 10.1007/s42000-021-00278-2

PURPOSE: Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods.
METHODS: Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R.
RESULTS: The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔGGBSA = -65.08 and ΔGPBSA = -87.62 kcal/mol) than for NPY1R (ΔGGBSA = -23.11 and ΔGPBSA = -50.56 kcal/mol).
CONCLUSIONS: Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.
Synthesis, molecular structure, FT-IR, Raman, XRD and theoretical investigations of (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one

Chidan Kumar CS, Fun HK, Parlak C, Rhyman L, Ramasami P, Tursun M, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2014 Nov 11;132:174-82.
PMID: 24858359 DOI: 10.1016/j.saa.2014.04.155

A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory method, employing, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P2₁/c with the unit cell parameters a=5.7827(8)Å, b=14.590(2)Å, c=16.138(2)Å and β=89.987 (°). The CC bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally.
(2E)-1-(5-Chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one: Synthesis, XRD, FT-IR, Raman and DFT studies

Parlak C, Ramasami P, Kumar CS, Tursun M, Quah CK, Rhyman L, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2015 Oct 5;149:385-95.
PMID: 25974671 DOI: 10.1016/j.saa.2015.04.022

A novel (2E)-1-(5-chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one [C21H15ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of HF, MP2, BP86, BLYP, BMK, B3LYP, B3PW91, B3P86 and M06-2X functionals. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the triclinic space group P-1 with the cis-trans-trans form. There is a good agreement between the experimentally determined structural parameters and vibrational frequencies of the compound and those predicted theoretically using the density functional theory with the BLYP and BP86 functionals.
Crystal structure, vibrational spectra and DFT simulations of 2-fluoro-4-bromobenzaldehyde

Tursun M, Kumar CS, Bilge M, Rhyman L, Fun HK, Parlak C, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2015 Jul 5;146:342-9.
PMID: 25829021 DOI: 10.1016/j.saa.2015.03.022

Molecular structure and properties of 2-fluoro-4-bromobenzaldehyde (FBB, C7H4BrFO) was experimentally investigated by X-ray diffraction technique and vibrational spectroscopy. Experimental results on the molecular structure of FBB were supported with computational studies using the density functional theory, with the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Molecular dimer formed by the intermolecular hydrogen bonding was investigated. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. FBB crystallizes in orthorhombic space group P2(1)2(1)2(1) with the O-trans conformation. In order to investigate halogen effect, the chloro- (CBB) and bromo- (BBB) analogs of FBB have also been studied theoretically. It is observed that all compounds prefer the stable O-trans conformation. Although the free energy difference between the O-cis and O-trans conformers is less than 2.5 kcal/mol, the free energy rotational barrier is at least 7.4 kcal/mol. There is a good agreement between the experimentally determined structural parameters, and vibrational frequencies of FBB and those predicted theoretically.
3-Iodobenzaldehyde: XRD, FT-IR, Raman and DFT studies

Kumar CS, Parlak C, Tursun M, Fun HK, Rhyman L, Ramasami P, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2015 Jun 15;145:90-7.
PMID: 25767992 DOI: 10.1016/j.saa.2015.02.079

The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X=F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed.